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I would belive that it would fit just fine without any mod's done to the engine bay do to the fact that there both 4.6 Ltr's however I have heard alot about the dohc's not really putting out without giving you headaches in the end. The way to do it is to port and polish that head and monifold if the manifold is aluminum at least, and do some head work new spring's lock's roller's and the whole kit can be picked up for a little over a hundred bux if you do your shopping right, then drop a good cam. Check out some other online forum's but if you just want to do the entire swap it should bolt right up...

yeah, that's great that you have the whole car for the swap. Ensure the computer is in good working order, but other than that, you might have to swap or slightly modify the wiring harness here or there. There should be a lot of info about this on Ford mod engine specific forums. Now gets to the researching and let see a GT sleeper come to life!

I'm currently putting a 97' Mark VIII 4.6 in 97' Cobra and I had to do was to change the wire harness,intake,valve covers. The most important change was the Mark VIII 6 bolt flywheel from the 8 bolt flywheel 5 speed Cobra tranny. I bought a 6 bolt kit(Mustang GT) and made the conversion.